Re: [PyMOL] display sdf data

Hi Sebastien,

If you have multiple poses of the same molecule in your sdf file, you
can translate them into a multi-model PDB file, writing the score and
rmsd values to the bfactor and occupancy field. This you can then load
into pymol, allowing you to step through the poses. With the command
'spectrum' you can colour according to b-factor or occupancy, allowing
a quick judgment of the quality of a certain pose.
I'm not sure if it will also work that way if the sdf file contains
different molecules.

Hope it helps,

Tsjerk

On Mon, Aug 30, 2010 at 9:51 AM, Sebastian Kruggel
<kr...@ch...> wrote:
> dear all,
>
> i try to find a way of displaying data about molecules
> contained in a sdf file (score and rmsd values of docked
> poses) - at the best as labels.
>
> in the mailing list i only find information about displaying
> the title or splitting the sdf. i would like to keep the
> multimolecular character of the file (to go through the
> poses) but display the data of the sdf. is there any way to
> do this?
>
> thanks in advance,
> sebastian
>
>
>
>
> --
> Sebastian Kruggel
> Institut für Pharmazie
> Bundesstr. 45 | Raum 112 (406)
> D 20146 Hamburg
>
> Tel:   +49 (0)40 42838-3626 (-3484)
> mail:  kr...@ch...
> http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands